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Experiences with Parallelizing a Bio-informatics Program on the Cell BE

Hans Vandierendonck UGent, Sean Rul UGent, Michiel Questier and Koen De Bosschere UGent (2008) Lecture Notes in Computer Science. 4917. p.161-175
abstract
The Cell Broadband Engine Architecture is a new heterogeneous multi-core architecture targeted at compute-intensive workloads. The architecture of the Cell BE has several features that are unique in high-performance general-purpose processors, such as static instruction scheduling, extensive support for vectorization, scratch pad memories, explicit programming of DMAs, mailbox communication, multiple processor cores, etc. It is necessary to make explicit use of these features to obtain high performance. Yet, little work reports on how to apply them and how much each of them contributes to performance.This paper presents our experiences with programming the Cell BE architecture. Our test application is Clustal W, a bio-informatics program for multiple sequence alignment. We report on how we apply the unique features of the Cell BE to Clustal W and how important each is to obtain high performance. By making extensive use of vectorization and by parallelizing the applicationacross all cores, we speedup the pairwise alignment phase of Clustal W with a factor of 51.2 over PPU (superscalar) execution. The progressive alignment phase is sped up by a factor of 5.7 over PPU execution, resulting in an overall speedup by 9.1.
Please use this url to cite or link to this publication:
author
organization
year
type
conference
publication status
published
subject
keyword
parallelization, Bio-informatics, Clustal W, Cell BE
in
Lecture Notes in Computer Science
volume
4917
issue title
High Performance Embedded Architectures and Compilers
pages
15 pages
publisher
Springer
place of publication
Berlin
conference name
Third International Conference HiPEAC 2008
conference location
Göteborg, Sweden
Web of Science type
Proceedings Paper
Web of Science id
000252961400011
ISSN
0302-9743
ISBN
978-3-540-77559-1
language
English
UGent publication?
yes
classification
P1
copyright statement
I have transferred the copyright for this publication to the publisher
id
679142
handle
http://hdl.handle.net/1854/LU-679142
date created
2009-06-05 10:44:21
date last changed
2009-07-03 08:44:09
@inproceedings{679142,
  abstract     = {The Cell Broadband Engine Architecture is a new heterogeneous multi-core architecture targeted at compute-intensive workloads. The architecture of the Cell BE has several features that are unique in high-performance general-purpose processors, such as static instruction scheduling, extensive support for vectorization, scratch pad memories, explicit programming of DMAs, mailbox communication, multiple processor cores, etc. It is necessary to make explicit use of these features to obtain high performance. Yet, little work reports on how to apply them and how much each of them contributes to performance.This paper presents our experiences with programming the Cell BE architecture. Our test application is Clustal W, a bio-informatics program for multiple sequence alignment. We report on how we apply the unique features of the Cell BE to Clustal W and how important each is to obtain high performance. By making extensive use of vectorization and by parallelizing the applicationacross all cores, we speedup the pairwise alignment phase of Clustal W with a factor of 51.2 over PPU (superscalar) execution. The progressive alignment phase is sped up by a factor of 5.7 over PPU execution, resulting in an overall speedup by 9.1.},
  author       = {Vandierendonck, Hans and Rul, Sean and Questier, Michiel and De Bosschere, Koen},
  booktitle    = {Lecture Notes in Computer Science},
  isbn         = {978-3-540-77559-1},
  issn         = {0302-9743},
  keyword      = {parallelization,Bio-informatics,Clustal W,Cell BE},
  language     = {eng},
  location     = {G{\"o}teborg, Sweden},
  pages        = {161--175},
  publisher    = {Springer},
  title        = {Experiences with Parallelizing a Bio-informatics Program on the Cell BE},
  volume       = {4917},
  year         = {2008},
}

Chicago
Vandierendonck, Hans, Sean Rul, Michiel Questier, and Koen De Bosschere. 2008. “Experiences with Parallelizing a Bio-informatics Program on the Cell BE.” In Lecture Notes in Computer Science, 4917:161–175. Berlin: Springer.
APA
Vandierendonck, H., Rul, S., Questier, M., & De Bosschere, K. (2008). Experiences with Parallelizing a Bio-informatics Program on the Cell BE. Lecture Notes in Computer Science (Vol. 4917, pp. 161–175). Presented at the Third International Conference HiPEAC 2008, Berlin: Springer.
Vancouver
1.
Vandierendonck H, Rul S, Questier M, De Bosschere K. Experiences with Parallelizing a Bio-informatics Program on the Cell BE. Lecture Notes in Computer Science. Berlin: Springer; 2008. p. 161–75.
MLA
Vandierendonck, Hans, Sean Rul, Michiel Questier, et al. “Experiences with Parallelizing a Bio-informatics Program on the Cell BE.” Lecture Notes in Computer Science. Vol. 4917. Berlin: Springer, 2008. 161–175. Print.